title: Omics-based identification of pathophysiological processes.
abstract: Owing to the growing knowledge about the cellular molecular network and its alterations in diseases, most of the diseases become considered as "systems distortion of the cellular molecular network". This view of diseases, which we call "systems pathology", has brought about a new usage of the disease Omics, that is, to identify the altered molecular network underlying the disease. In this chapter, we discuss the technologies and clinical applications for Omics-based identification of pathophysiological process. In doing so, we classify the methods into two classes: one is a "data-inductive approach" which infers gene regulatory and transcriptional networks by gene expression data from DNA microarrays, and the other is a "knowledge-referenced approach" which combines the differentially expressed genes from gene expression profiles with existing protein interaction networks or literature-curated pathways. Several typical methods such as ARACNe and eQTL are described with their recent clinical applications.
authors.affiliation: Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan. tanaka@cim.tmd.ac.jp
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tanaka
authors.forename: Soichi
authors.initials: S
authors.lastname: Ogishima
mesh_terms: D053263:Gene Regulatory Networks; D006801:Humans; D010336:Pathology / Q000379:methods*; D057285:Precision Medicine; D011315:Preventive Medicine; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration